search this blog

Friday, September 30, 2016

Abstract: Dramatic events in human prehistory, such as the spread of agriculture to Europe from Anatolia and the Late Neolithic/Bronze Age (LNBA) migration from the Pontic-Caspian steppe, can be investigated using patterns of genetic variation among the people that lived in those times. In particular, studies of differing female and male demographic histories on the basis of ancient genomes can provide information about complexities of social structures and cultural interactions in prehistoric populations. We use a mechanistic admixture model to compare the sex-specifically-inherited X chromosome to the autosomes in 20 early Neolithic and 16 LNBA human remains. Contrary to previous hypotheses suggested by the patrilocality of many agricultural populations, we find no evidence of sex-biased admixture during the migration that spread farming across Europe during the early Neolithic. For later migrations from the Pontic steppe during the LNBA, however, we estimate a dramatic male bias, with ~5-14 migrating males for every migrating female. We find evidence of ongoing, primarily male, migration from the steppe to central Europe over a period of multiple generations, with a level of sex bias that excludes a pulse migration during a single generation. The contrasting patterns of sex-specific migration during these two migrations suggest a view of differing cultural histories in which the Neolithic transition was driven by mass migration of both males and females in roughly equal numbers, perhaps whole families, whereas the later Bronze Age migration and cultural shift were instead driven by male migration, potentially connected to new technology and conquest.

Monday, September 26, 2016

Published along with Pagani et al. 2016, the EGDP dataset is freely available at the Estonian Biocentre website as VCF and PLINK binary files here. It overlaps at ~550K SNPs with Broad MITs/Harvard's Human Origins, and at an impressive ~1.1 million SNPs with the ~1.2 million SNP ancient DNA chip used by the Reich Lab and others.
To see what's what, I ran a Principal Component Analysis (PCA) of all of the samples except the Congo Pygmies. I then removed four Siberians that behaved as if they had very recent European ancestry, and reran the PCA. Below are a few screen grabs from the latter analysis. The datasheet is available here.

I also tested a few of the samples with my Basal-rich K7 model. You can see their results in the spreadsheet here. Look for the individual IDs with the GS prefix.
Using the K7 spreadsheet and nMonte, here's a model for Ashkenazi Jews with some of the new EGDP populations as references, including Avars from the North Caucasus and Arabs from Israel. The Arabs do help to improve the fit, but they're not as important as Samaritans and Tuscans.

Thursday, September 22, 2016

All comments posted here must comply with the following rules. Comments that break these rules will be removed. Repeat offenders will be banned.

- no racial or ethnic taunts and insults
- do not for any reason speculate about the people posting here
- avoid discussions with obvious trolls and/or mentally unstable people*
- no conspiracy theories
- do some reading here before posting if unfamiliar with the relevant topics
- do not post any illegal or defamatory material
- stay on topic unless you have a good excuse for going off topic

*Mental illness is not a joke, but it is a reality for a lot of people, so we're bound to see some visitors here occasionally with this problem. If unsure, simply ignore and move on.
There is no rule against swearing and name calling, but try to keep things civil. Trolls should be regularly called out for who they are, but keep it short and then move on.
See also...
Banned commentators list

Wednesday, September 21, 2016

A robust but healthy debate by proxy between three teams of population geneticists over at Nature today. Emphasis is mine:

Absract: High-coverage whole-genome sequence studies have so far focused on a limited number1 of geographically restricted populations (2, 3, 4, 5) or been targeted at specific diseases, such as cancer6. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history (7, 8, 9) and refuelled the debate on the mutation rate in humans (10). Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record (11), and admixture between AMHs and Neanderthals predating the main Eurasian expansion (12), our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.

Abstract: Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.

Abstract: The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama–Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25–40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10–32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama–Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51–72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.

Thursday, September 15, 2016

PLoS One has a new paper on a Mongolian imperial tomb dated to 1130–1250 AD, which is the early Mongolian era. Here's the table with the Y-haplogroup results:

The authors make the sensible conclusion that these Mongolians had paternal ancestry from somewhere in Western Eurasia. But they also make this stupid comment:

Similarly, the high frequency of R1b-M343 in geographic regions associated with the past Mongol khanates including the Golden Horde (from Ural Mountain to Western Siberia, which includes Russia, Ukraine, Belarus, Poland, Azerbaijan, Kazakhstan, and Uzbekistan), Ilkhanate (Iran and neighboring territories including Armenia, Turkey, Georgia, Afghanistan, Syria, and Tajikistan), and Chagatai Khanate (from the Aral sea to the Altai mountain, including Pakistan (Hazara), Uzbekistan, Kazakhstan, Tajikistan, India, and China), strongly suggest a close association between the Y haplotype R1b-M343 and the past Mongol Empire.

No, the distribution, frequencies and subclades of R1a or R1b do not show any sort of meaningful correlation with the past Mongol Empire.
The most obvious explanation, although not the only possible one, for the presence of R1a and R1b lineages in Mongolian imperial remains are the migrations of the Afanasievo and/or Andronovo people into the Altai region from the Eastern European steppes during the Bronze Age. See here...

Tuesday, September 13, 2016

The abstract book for this week's meeting is available here. Emphasis is mine. The two abstracts on the genetic shifts in the East Baltic region might look as if they contradict each other, but they don't. What they're suggesting is that the East Baltic was basically home to typical European hunter-gatherers right up until the Late Neolithic, when the Corded Ware people crashed into the area, probably from the steppe via East Central Europe. For more on this topic also see here.

Mitochondrial DNA Analysis of Human Remains from Estonia
Pfrengle et al.
The transition from hunter-gatherer subsistence to farming is one of the most important processes in human history. In Europe, it has been found to be a result of demic diffusion originating from the Near East. The arrival of the first farmers in Europe lead to an increase of genetic diversity as well as genetic admixture of local hunter-gatherer and the migrating farmers. Previous studies investigating European human history using mitochondrial and genome-wide nuclear data from early farmers and hunter-gatherers have provided detailed insights into the process of admixture and replacement throughout the Neolithic period. However this process has been poorly studied in the Baltic region where archaeological research suggests more extensive scenarios. Here we reconstructed the complete mtDNA of 19 individuals from different archaeological sites of Estonia covering the timespan from the Narva Culture to the Corded Ware Culture and determined their mitochondrial haplogroups. The results show that the typical European hunter-gatherer maternal lineages are represented exclusively in all individuals from until the Middle Neolithic. From the Late Neolithic on, haplogroups that are associated with European Neolithic farmers are detected. The results indicate genetic continuity of foraging cultures of Mesolithic and early Neolithic backgrounds and a late demic diffusion into the territory of Estonia associated with people of the Corded Ware culture. In addition, the generated genetic data are used to gain insights into the demography of burial complexes by sex determination and maternal kinship analysis.
The Neolithic Transition at the Edge of Europe
Jones et al.
In Europe, the Neolithic transition marked the beginning of a period of innovations which saw people move from a mobile lifestyle, dependent on hunting and gathering for survival, to a more sedentary way of life based on food production. This new lifeway, which began in the Near East ~11 kya, spread quickly across the continental interior of Europe predominantly through demic diffusion.
While the genetic impact of the Neolithic transition has been well explored in central Europe, its impact on more peripheral regions of the continent has not been as extensively studied. To broaden our understanding of this dynamic phase in European prehistory, we analysed genomes from a 4,000 year temporal transect through the Baltic region spanning from the Late Mesolithic to the Late Neolithic period. We found evidence for connectivity from the Mesolithic to the Neolithic however, we also detected signals consistent with influxes from non-local populations. These influences were distinct from the early farmer admixture which transformed the genetic landscape of central Europe during the Neolithic. Interestingly, dietary stable isotope analyses (δ15N and δ 13C) show that the genetic shifts coincide with diversifications in subsistence strategy. These results suggest that the Neolithic was a period of genetic flux in the Baltic however, the cultural and technological changes observed were largely independent of forager-farmer genetic exchange.Reconstructing population history in East Asia
Wang et al.
The deep population history of East Asia remains poorly understood compared to that of West Eurasia, due to the lack of ancient DNA data as well as limited sampling of present-day populations especially on the Tibetan Plateau and in southern China. We report a fine scale survey of East Asian history based on genome-wide data from ancient samples in the Amur River Basin, as well as 435 newly reported individuals from 53 populations. Present-day groups can be broadly classified into highly differentiated clusters, corresponding to Amur River Basin, Tibetan Plateau, southern natives and Han Chinese. Populations of the Amur River Basin show a high degree of genetic continuity from seven thousand years ago until today, and are closely related to the strain of East Asian related ancestry present in Native Americans. Tibetan Plateau populations are all admixed, deriving about 5%-10% of their ancestry from an anciently divergent population that plausibly corresponds to the Paleolithic population on the Plateau, and the remaining part from an ancient population that no longer exists in unmixed form but that likely corresponds to expanding farmers from the Middle and Upper Yellow River Basin who also contributed 40-90% of the ancestry of Han Chinese. A total of 10-60% of Han Chinese ancestry derives from southern Native populations, and we show that the type of southern Native ancestry that contributed to Taiwan Island Austronesian speakers is most closely related to present-day speakers of Tai-Kadai languages in southern mainland China.
Contextualizing the Tianyuan genome within present and ancient human genomic diversity
Yang et al.
Recently, many studies have produced an unprecedented number of ancient human genomes, providing insight on human dynamics in many regions, particularly West Eurasia and the Americas. Here, we present genome-wide data from the Tianyuan specimen, dating to ~40,000 years ago. Unlike other ancient genomes studied to date, the Tianyuan genome is the first ancient Upper Paleolithic sample analyzed to have contributed greatly to the East Eurasian ancestral lineage. We compare Tianyuan to several ancient and present day human genomes to better understand both the genetic diversity in the Upper Paleolithic and the similarities and differences between Tianyuan and present day populations. Overall, the addition of genome-wide Tianyuan data provides greater insight into the population history in Eurasia over the last 40,000 years.
Capture of ancient genomic DNA of individuals recovered from a Medieval Alemannic gravesite provides evidence for high mobility of fellowships during the 7th century CE.
O'Sullivan et al.
Whether the historic spread of cultural/language groups such as the Alemanni were migrations or local adoption of culture is still unresolved in archaeology. The Alemanni were a confederation of tribes that inhabited an area, from the third to the 10th century CE, which approximately overlaps with the modern distribution of Alemannic German dialect in Swabia. We present the genomic and isotopic data of eight individuals excavated from a gravesite in Niederstotzingen, Germany of supposed Alemannic origin dated to the 7th century CE. There were two multiple burials at the site suggesting either kinship or fellowship between the individuals. The tombs in the gravesite contained cultural artefacts and weapons indicating close contact of the Alemanni with Longobards and Byzantines. We investigated the genetic affinity of these individuals between each other and to modern West Eurasians. The genetic analysis utilised the targeted enrichment and sequencing of over 1.2 million genetic markers that have known ascertainment. From these data, we found no familial relationship among the individuals in the multiple graves, thus supporting a burial practice based rather on fellowship. All individuals were genetically male. The genetic affinities of the individuals, based on modern genetic distributions, were five Eastern Europeans, two Germans/Austrians and one Southern European. Isotopic data supports that only the Southern European individual was certainly born outside this region. The genetic data appear to correlate with the provenance of the burial artefacts, showing that westward movements and interactions among cultural groups likely occurred in this region during the 7th century CE.
Origins and genetic legacy of the first people in Remote Oceania
Skoglund et al.
The appearance of people associated with the Lapita culture in the South Pacific ~3,000 years ago marked the beginning of the last major human dispersal to unpopulated lands, culminating in the settlement of eastern Polynesia ~1,000-700 years ago. However, the genetic relationship of these pioneers to the long established Papuan peoples of the New Guinea region is debated. We report the first genome-wide ancient DNA data from Asia-Pacific region, from four ~2,900 to ~2,500 year old Lapita culture individuals from Vanuatu and Tonga, and co-analyze them with new data from 356 present-day Oceanians. Today, all indigenous people of the South Pacific harbor a mixture of ancestry from Papuans and a population of East Asian origin that we find to be a statistical match to the ancient Lapita individuals. Most analyses have interpreted the ubiquitous Papuan ancestry in the region today-at least 25%-as evidence that the first humans to reach Remote Oceania and Polynesia were derived from mixtures near New Guinea prior to the Lapita expansion into Remote Oceania. Our results refute this scenario, as none of the geographically and temporally diverse Lapita individuals had detectable Papuan ancestry. These results imply later major human population movements, which spread Papuan ancestry through the South Pacific after the islands' first peopling.An ancient genomic perspective on the horse domestication process
Librado et al.
The domestication of the horse in the Pontic-Caspian steppes some 6,000 years ago represents one major turning point in human history. With horses, humans could travel for the first time well above their own speed and carry their germs, culture and genes across vast geographic areas. The development of horse-drawn chariots and cavalry also radically changed the history of warfare and was instrumental to the emergence of transcontinental empires. Additionally, beyond the battlefield, farm horses have massively impacted agricultural productivity. The biological changes that accompanied the process of horse domestication are, however, difficult to reconstruct from current patterns of genetic diversity both due to the development of intensively selected and extremely influential breeds during the last two centuries, and the almost extinction of wild horses. Recent developments in ancient DNA research have opened for the characterization of complete genomes, epigenomes and microbiota over long time series. We have applied such approaches to a large panel of horse remains spread across Eurasia and dated to 44,000-200 years ago. This started revealing the genetic structure of horse populations prior to and during early domestication stages as well as the history of genetic changes that accompanied their further transformation in a range of cultural contexts. I will present our latest progress made on an extensive dataset of ancient horse genomes spanning the whole domestication temporal and geographical range.
Mobility between the Aegean and the Levant in the Late Second Millennium BCE: inference from ancient DNA of pigs
Meiri et al.
The Late Bronze and the early Iron Ages (ca. 1450-950 BCE) of the eastern Mediterranean region are characterized by dramatic historical processes. Empires emerged and collapsed, trade connections were established and severed, and at the end of this era socio-political unrest and migration of large groups of people were rife throughout the region. In the 12th century BCE the movements of the so-called "Sea Peoples" affected wide parts of the East Mediterranean. We study the nature of human movements during this period on trade connections, culture and animal husbandry using the ancient DNA of domestic animals, above all pigs. We recently showed that in Israel, European pig haplotypes appeared ca. 900 BCE, and soon after took over the gene pool, with all modern wild boars in Israel carrying European mitochondrial DNA. Here, we broadened the chronological and spatial scopes by studying ancient pig mitochondrial DNA from the southern Levant and Greece. The Near Eastern haplotype Y1 and supposedly Near Eastern haplotype Y2 were discovered in Greece in the mid to late 3rd millennium BCE, while the European haplotypes were found in Israel in the early Iron Age IIA (ca. 900 BCE). We propose that pigs were moved between Europe and Anatolia since the early Bronze Age. Connections between Greece and the southern Levant are observed in the Iron Age, and probably result from the migration of Sea Peoples to the east. These results shed light on networks and movements of people during both times of prosperity and crisis.

Interesting stuff from the ADNABIOARC team at Scientific Reports today:

Abstract: The Neolithic transition brought about fundamental social, dietary and behavioural changes in human populations, which, in turn, impacted skeletal morphology. Crania are shaped through diverse genetic, ontogenetic and environmental factors, reflecting various elements of an individual’s life. To determine the transition’s effect on cranial morphology, we investigated its potential impact on the face and vault, two elements potentially responding to different influences. Three datasets from geographically distant regions (Ukraine, Iberia, and the Levant plus Anatolia) were analysed. Craniometric measurements were used to compare the morphology of pre-transition populations with that of agricultural populations. The Neolithic transition corresponds to a statistically significant increase only in cranial breadth of the Ukrainian vaults, while facial morphology shows no consistent transformations, despite expected changes related to the modification of masticatory behaviour. The broadening of Ukrainian vaults may be attributable to dietary and/or social changes. However, the lack of change observed in the other geographical regions and the lack of consistent change in facial morphology are surprising. Although the transition from foraging to farming is a process that took place repeatedly across the globe, different characteristics of transitions seem responsible for idiosyncratic responses in cranial morphology.

Sunday, September 11, 2016

Below are a couple of images from two unsupervised analyses featuring a variety of ancient and present-day Eurasians (and one ancient American). The results should be self-explanatory. Click on the images to download high resolution versions. The Principal Component Analysis (PCA) datasheet is available here.
I'm using fully homozygous sequences. Most of the ancient samples are composites to maximize the number of markers (over 400K SNPs). All of the ancient samples and almost all of the present-day samples are freely available at the Reich Lab website here, but in some cases with fewer markers than what I'm using.

Let me just reiterate, this is an unsupervised analysis; TreeMix is simply told to find the best fitting migration edge in the data, and it does the rest, showing the ancient American, Clovis, as a mixture of East and West Eurasians. To be honest, I'm blown away by the accuracy of these results and the strong correlation between the PCA and TreeMix graph.

Thursday, September 8, 2016

The American Society of Human Genetics (ASHG) 2016 Meeting Online Planner and Abstract Search can be accessed here. Unless I'm missing something, there's surprisingly little ancient genomics stuff this year considering the huge advances in this area recently.

However, Iain Mathieson has an interesting contribution about interactions between Balkan foragers and early Balkan farmers. Reading between the lines, I reckon we can probably expect some R1b in these Balkan ancients. This shouldn't be surprising, however, considering the publication earlier this year of the Ice Age Villabruna genome from present-day northeast Italy, which belonged to R1b and, as pointed out by myself, also showed strong genome-wide ties to ancient Siberians (see here).

Oleg Balanovsky has been acting a little strange lately; seemingly going out of his way to fight the Kurgan Indo-European paradigm in various papers and talks. In this poster he underlines the fact that the Yamnaya people from the North Caspian region did not totally vacate their homeland nor moved en masse to Western Europe, but actually left most of their descendants in the North Caspian. OK Oleg, but almost all modern day Europeans, especially those from across Northern and Eastern Europe, do derive a lot of their ancestry from Bronze Age steppe groups closely related to the Yamnaya people of the North Caspian. This will become even more obvious soon with the publication of new ancient data from the Baltic region.

And here we have what appears to be yet another hilariously wrong paper in the making on the population history of South Asia. Why do they mention Anatolia? How about the Arctic Circle? Enough already. Get some goddamn ancient genomes from South Asia and finally do it right.

Friday, September 2, 2016

Just wanted to see what would happen if I split Ust-Ishim into two homozygous sequences, and ran him in a Principal Component Analysis (PCA) alongside other fully homozygous individuals and composites, both modern day and ancient. In theory this shouldn't be a problem, considering that his genome is of such an incredibly high quality (~42-fold coverage). The datasheets for the PCA below are available here and here.
This is the only way that I can think of to run a PCA in which genetic drift specific to the Ust'-Ishim population of ~45K YBP western Siberia has a clear impact. Indeed, lots of interesting things on these plots. Note, for instance, that on the second plot the Afanasievo and Yamnaya-Catacomb composites appear to be attracted to the Caucasus Hunter-Gatherer composite. Also note how unusual the Neolithic Iranians (Iran_EN) appear.

Update 02/09/2016: Interactive 3D versions of these PCA are now available at Open Genomes here and here. Below are screen caps of angles that appear to recapitulate the geography of Eurasia. See comments below for details.